In 2015 Scrutton co-founded the company C3 Biotechnologies Ltd to commercialise technologies for fuels and chemicals production using synthetic biology. He is Director of the Manchester Synthetic Biology Research Centre SYNBIOCHEM, which he established in 2014 following major investment by the UK government in synthetic biology. He is also Director of the Future Biomanufacturing Research Hub established in 2019, which is developing new technologies to accelerate bio-based manufacturing in the UK in three key sectors – pharmaceuticals, chemicals and engineering materials. He has served on several national committees, including research council / funding committees (BBSRC, EPSRC, Royal Society) and strategic advisory boards / scientific steering groups (e.g. Science and Technology Facilities Council).